package analysis;


/**
 * @author Mathieu Rousseau
 * @email mathieu.rousseau3@mail.mcgill.ca
 */


/** ------------------------------------------------------------------------------------------------------------------
 * start of MicrocosmMain class
 * ------------------------------------------------------------------------------------------------------------------  **/
public class MicrocosmMain {

	/*  start of main method  */
	public static void main(String[] args) {
		
		
		
		//  parameters for the MCMC5C program
		String experimentName, filenameFragments;
		int numberOfStructures, resolution;
		double radius;
		
		
		//  create the Microcosm object
		Microcosm analyzer = new Microcosm();
		
		
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		//  specify the experiment name which is the suffix in the naming convention for structures: "structure_####_experimentName.pdb"
//		experimentName = "MCMC5C_DMSO";
//		experimentName = "DMSO[5]";
		experimentName = "PMA[2]";
		//  if there is no experiment name and the structures are exactly named "structure_####.pdb" then can specify the experiment name as "none"
//		experimentName = "none";
		
		
		//  specify the file that contains the genomic locations corresponding to each of the fragments (endpoints) in the structures 
		filenameFragments = "fragments.txt";
		
		
		//  set the number of structures to analyze
		numberOfStructures = 100;
		
		
		//  set the level of resolution
		resolution = 10;
		
		
		//  set the radius
		radius = 1;
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								END OF HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		
		
		//  add all of the parameters to the arguments array
		args = new String[5];
		args[0] = experimentName;
		args[1] = filenameFragments;
		args[2] = String.valueOf(numberOfStructures);
		args[3] = String.valueOf(resolution);
		args[4] = String.valueOf(radius);
		

		//  run the Microcosm analysis
		analyzer.run(args);
		
	}/*  end of main method  */

}/*  end of MicrocosmMain class  */
